4-2744887-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024309.4(TNIP2):āc.716G>Cā(p.Arg239Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,566 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R239S) has been classified as Uncertain significance.
Frequency
Consequence
NM_024309.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNIP2 | NM_024309.4 | c.716G>C | p.Arg239Thr | missense_variant | 4/6 | ENST00000315423.12 | |
TNIP2 | NM_001161527.2 | c.395G>C | p.Arg132Thr | missense_variant | 4/6 | ||
TNIP2 | NM_001292016.2 | c.658-381G>C | intron_variant | ||||
TNIP2 | XM_047416149.1 | c.337-381G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNIP2 | ENST00000315423.12 | c.716G>C | p.Arg239Thr | missense_variant | 4/6 | 1 | NM_024309.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152274Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461292Hom.: 0 Cov.: 34 AF XY: 0.0000124 AC XY: 9AN XY: 726878
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.716G>C (p.R239T) alteration is located in exon 4 (coding exon 4) of the TNIP2 gene. This alteration results from a G to C substitution at nucleotide position 716, causing the arginine (R) at amino acid position 239 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at